Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,713,436	C→G	7.0%	S374T (AGT→ACT)	paaK ←	phenylacetate‑CoA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,713,436	0	C	G	7.0%	180.6 / 4.8	57	S374T (AGT→ACT)	paaK	phenylacetate‑CoA ligase
Reads supporting (aligned to +/- strand):  ref base C (28/25);  new base G (2/2);  total (30/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.67e-01

GTGCCGCAGGGCTGCAGGTGCACCTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGCCGGTGATCTTGC  >  NC_002947/3713295‑3713580                                                                                                                                              |                                                                                                                                                 gTGCCGCAGGGCTGCAGGTGCACCTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGa                                                                                                                                          <  1:1023697/150‑1 (MQ=255)  tGCCGCAGGGCTGCAGGTGCACCTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAggt                                                                                                                                         <  1:451500/150‑3 (MQ=255)          ggCTGCAGGTGCACCTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTg                                                                                                                                 <  2:242209/150‑1 (MQ=255)                  gTGCACCTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTcc                                                                                                                                             <  2:888993/130‑1 (MQ=255)                  gTGCACCTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTcc                                                                                                                                             >  1:888993/1‑130 (MQ=255)                       ccTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGaa                                                                                                                    <  1:271998/150‑1 (MQ=255)                        cTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACAGTGTCCAggtg                                                                                                                                        >  2:180150/1‑126 (MQ=255)                        cTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACAGTGTCCAggtg                                                                                                                                        <  1:180150/129‑4 (MQ=255)                        cTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACt                                                                                                                                                 >  1:746701/1‑120 (MQ=255)                        cTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACt                                                                                                                                                 <  2:746701/120‑1 (MQ=255)                                tGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATaaa                                                                                                           >  2:1135416/1‑150 (MQ=255)                                     ccGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTCGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCa                                                                                                      <  1:92916/150‑1 (MQ=255)                                       gATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCa                                                                                                      <  1:804079/148‑1 (MQ=255)                                       gATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCa                                                                                                      >  2:804079/1‑148 (MQ=255)                                                    aTCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCa                                                                                                      <  1:203381/135‑1 (MQ=255)                                                    aTCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCa                                                                                                      >  2:203381/1‑135 (MQ=255)                                                      cTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACAGTGTCCAggt                                                                                                                                         <  2:157680/98‑3 (MQ=255)                                                      cTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACAGTGTCCAggt                                                                                                                                         >  1:157680/1‑96 (MQ=255)                                                       tgcttgctCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCAtt                                                                                                                                  <  1:1340894/104‑1 (MQ=255)                                                       tgcttgctCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCAtt                                                                                                                                  >  2:1340894/1‑104 (MQ=255)                                                              tCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCt                                                                             >  1:646818/1‑150 (MQ=255)                                                                   tCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGTGATACAGAt                                                                                                                       <  2:199214/103‑1 (MQ=255)                                                                   tCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGAt                                                                                                                       >  1:199214/1‑103 (MQ=255)                                                                    ccccGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCt                                                                       >  2:10379/1‑150 (MQ=255)                                                                            aCCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGa                                                               >  2:884855/1‑150 (MQ=255)                                                                              cAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGACAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGt                                                             >  1:213983/1‑150 (MQ=255)                                                                                gCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCg                                                           <  2:1264306/150‑1 (MQ=255)                                                                                  ttGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCggg                                                         >  1:669307/1‑150 (MQ=255)                                                                                    gcgcTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGaa                                                       <  2:669307/150‑1 (MQ=255)                                                                                          gCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTAttttt                                                                                    <  1:1263926/115‑1 (MQ=255)                                                                                          gCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTAttttt                                                                                    >  2:1263926/1‑115 (MQ=255)                                                                                            ccTCGTCAAGGTGCTAACACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGa                                               >  1:1047485/1‑150 (MQ=255)                                                                                             cTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGAc                                              >  2:810819/1‑150 (MQ=255)                                                                                                      gTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCt                                                                                               >  2:726737/1‑92 (MQ=255)                                                                                                      gTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCt                                                                                               <  1:726737/92‑1 (MQ=255)                                                                                                         cTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCcgc                                         >  1:816116/1‑143 (MQ=255)                                                                                                         cTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCcgc                                         <  2:816116/143‑1 (MQ=255)                                                                                                          tGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGa                                                                                                                        <  1:570888/63‑1 (MQ=255)                                                                                                          tGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGa                                                                                                                        >  2:570888/1‑63 (MQ=255)                                                                                                          tGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCggg                                                         <  1:522741/126‑1 (MQ=255)                                                                                                          tGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCggg                                                         >  2:522741/1‑126 (MQ=255)                                                                                                          tGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATc                                 >  1:539412/1‑150 (MQ=255)                                                                                                            gCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGaa                                                       >  1:497101/1‑126 (MQ=255)                                                                                                            gCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGaa                                                       <  2:497101/126‑1 (MQ=255)                                                                                                            gCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAg                               >  1:487919/1‑150 (MQ=255)                                                                                                              aCTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCa                             <  1:884855/150‑1 (MQ=255)                                                                                                                  tGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATgtc                         <  1:810819/150‑1 (MQ=255)                                                                                                                              cACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCa                                <  2:629787/131‑1 (MQ=255)                                                                                                                              cACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCa                                >  1:629787/1‑131 (MQ=255)                                                                                                                              cACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGcc             >  2:389888/1‑150 (MQ=255)                                                                                                                                 gTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGCCGGt          >  1:795029/1‑150 (MQ=255)                                                                                                                                     aCCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGCCGGTGATc      >  2:1382850/1‑150 (MQ=255)                                                                                                                                       cTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAac                                                      <  2:404671/100‑1 (MQ=255)                                                                                                                                       cTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAac                                                      >  1:404671/1‑100 (MQ=255)                                                                                                                                       cTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGCCGGTGATCtt    >  1:1212608/1‑150 (MQ=255)                                                                                                                                        tGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGCCGGTGATCTTg   <  1:10379/150‑1 (MQ=255)                                                                                                                                         ggACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGCCGGTGATCTTGc  <  2:116516/150‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                 GTGCCGCAGGGCTGCAGGTGCACCTGGGTGCTGATACCGATGTAAGTCTTGATCTGCTTGCTCAACTCCCCGACAACCAGCTTGCGCTGGCCCTCGTCAAGGTGCTGGCACTCTGCACGCAGCTCCACGTGCACCTGGACACTGTCCAGATTTCCATTGCGATACAGATGAATCTCATAAAGCTCAGAAAGCTGTTTTATTTTTAGCACCTGTTCCTCGATCTGAGTCGGGAACACATTGACCCCGCGAATGATCAGCATGTCGTCACTGCGGCCGGTGATCTTGC  >  NC_002947/3713295‑3713580

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑